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Large aggregation#192

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kclem merged 67 commits intopinellolab:masterpinellolab/CRISPResso2:masterfrom edilytics:largeAggregationedilytics/CRISPResso2:largeAggregationCopy head branch name to clipboardMay 4, 2022

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Commits on Jan 11, 2022

• Squashed commit of the following:

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Commits on Jan 13, 2022

• Merge branch 'pinellolab:master' into master

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Commits on Jan 23, 2022

• Add parameter --suppress_batch_summary_plots

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• Pep formatting cleanup

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• Add summary nucleotide plots to aggregate

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• Aggregate plots are paginated

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• Update CRISPRessoAggregateCORE.py

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Commits on Jan 24, 2022

• Add --max_samples_per_summary_plot to CRISPRessoAggregate

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Commits on Jan 26, 2022

• Add plotly function to plot an interactive heatmap

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• Fix deprecated numpy type to suppress warning

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• Add plotting of heatmaps to CRISPRessoAggregateCORE to summarize modification types

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• Add the heatmap summaries to the CRISPRessoAggregate report

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Commits on Jan 28, 2022

• Update Bootstrap to 5.1.3

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Commits on Jan 29, 2022

• Move the plotly heatmaps to a Bootstrap modal

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Commits on Mar 15, 2022

• Merge branch 'master' of https://github.com/edilytics/CRISPResso2

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• Fix bug where plots were not filling up entire modal.

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Commits on Mar 16, 2022

• Update the axis labels and add autosize to plotly heatmaps

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• Abandon attempts to make plots fullscreen

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Commits on Mar 18, 2022

• Rename and refactor how plot data is passed around

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Commits on Mar 22, 2022

• Implement the line plot version of the modification percentages

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• Change default max_samples_per_summary_plot to be 150 instead of 250

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• Remove extra assignments of this_number_samples and suppress plot

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Commits on Mar 23, 2022

• Implement parallel plotting in CRISPRessoAggregate

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• Fix sample indexing error and heatmap scaling for large number of samples

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Commits on Mar 25, 2022

• Merge branch 'pinellolab:master' into master

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• Add parameter --suppress_batch_summary_plots

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• Pep formatting cleanup

  

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• Add summary nucleotide plots to aggregate

  

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• Aggregate plots are paginated

  

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• Update CRISPRessoAggregateCORE.py

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• Add --max_samples_per_summary_plot to CRISPRessoAggregate

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• Add plotly function to plot an interactive heatmap

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• Fix deprecated numpy type to suppress warning

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• Add plotting of heatmaps to CRISPRessoAggregateCORE to summarize modification types

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• Add the heatmap summaries to the CRISPRessoAggregate report

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• Update Bootstrap to 5.1.3

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• Move the plotly heatmaps to a Bootstrap modal

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• Fix bug where plots were not filling up entire modal.

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• Update the axis labels and add autosize to plotly heatmaps

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• Abandon attempts to make plots fullscreen

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• Rename and refactor how plot data is passed around

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• Implement the line plot version of the modification percentages

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• Change default max_samples_per_summary_plot to be 150 instead of 250

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• Remove extra assignments of this_number_samples and suppress plot

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• Implement parallel plotting in CRISPRessoAggregate

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• Fix sample indexing error and heatmap scaling for large number of samples

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Commits on Mar 27, 2022

• Merge branch 'largeAggregation' of https://github.com/edilytics/CRISPResso2 into largeAggregation

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• Add plotly requrement to setup.py

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• Remove space around vertical barcharts

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• Add scrollbar to long images in multiReport

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Commits on Mar 28, 2022

• Fill in default (empty) values to allele modification plots

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Commits on Mar 29, 2022

• Include CRISPRessoBatch in the refactor of how summary_plot dicts are handled

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Commits on Apr 8, 2022

• Update dockerfile for new docker

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Commits on May 2, 2022

• minor bug fixes for plotCustomAllelePlot.py to work with Python3 (pinellolab#212)

  

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• Allow for flexible parsing of quant window coordinates

  

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• CRISPRessoPooled debug flash command, fix pep formatting

  

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• Set flexiguide homology parameter type to int

  

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• Coerce ints in batch file checking (pinellolab#200)

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• Handle multiple qwcs in batch mode

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• Fix bug from old pandas for int cols

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• Merge branch 'pinellolab:master' into master

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Commits on May 3, 2022

• Merge branch 'master' into largeAggregation

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• Create allele modification heatmaps and line plots in CRISPRessoBatch

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• Add allele modification heatmaps and line plots to CRISPRessoBatch

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• Make all plots in CRISPRessoBatch run in parallel

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• Make --suppress_batch_summary_plots store true

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• Add blank values for allele_modification entries when not present

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